Makefile
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 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC  := $(shell basename `pwd`)
 
 all: rd readme check clean
 
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 alldocs: site rd readme
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 rd:
 	Rscript -e 'roxygen2::roxygenise(".")'
 
 readme:
 	Rscript -e 'rmarkdown::render("README.Rmd")'
 
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 sticker:
 	Rscript -e 'source("ggtree_sticker.R")';
 	rm Rplots.pdf
 
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 build:
 	cd ..;\
 	R CMD build $(PKGSRC)
 
 build2:
 	cd ..;\
 	R CMD build --no-build-vignettes $(PKGSRC)
 
 install:
 	cd ..;\
 	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
 
 check: build
 	cd ..;\
 	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
 
 check2: build
 	cd ..;\
 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
 
 bioccheck:
 	cd ..;\
 	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
 
 clean:
 	cd ..;\
 	$(RM) -r $(PKGNAME).Rcheck/
 
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 site:
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 	cd site_src;\
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 	ln -s ../../software/themes themes;\
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 	Rscript -e 'blogdown::build_site()';\
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 	rm themes;\
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 	cd ..
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 preview:
 	Rscript -e 'setwd("site_src"); blogdown::serve_site()'
 
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 mkdocs: mdfiles
 	cd mkdocs;\
 	mkdocs build;\
 	cd ../docs;\
 	rm -rf fonts;\
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 	rm -rf css/font-awesome*
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 mdfiles:
 	cd mkdocs;\
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 	Rscript -e 'source("render.R")';\
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 	cd docs;\
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 	ln -f -s ../mysoftware/* ./
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 svnignore:
 	svn propset svn:ignore -F .svnignore .
 
 svncommit:
 	git checkout devel;\
 	git svn rebase;\
 	git merge master --log;\
 	git svn dcommit;\
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 	git push -u origin devel;\
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 	git checkout master;\
 	git merge devel
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 gitmaintain:
 	git gc --auto;\
 	git prune -v;\
 	git fsck --full
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 pushX:
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 	git push -u origin master;\
 	git checkout bioc;\
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 	git pull;\
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 	git merge master;\
 	git push upstream master;\
 	git checkout master
 
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 update:
 	git fetch --all;\
 	git checkout master;\
 	git merge upstream/master;\
 	git merge origin/master
 
 push: update
 	git push upstream master;\
 	git push origin master